Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2736

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5550
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31


Found at i:4079 original size:38 final size:39

Alignment explanation


    Indices: 3979--4201  Score: 240
    Period size: 40  Copynumber: 5.6  Consensus size: 39

       3969 TTGAATGATG

                                         *         *  
       3979 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
          1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT

                  *      *               *           
       4018 ATCCGGACTAAGATCCGAAGGCATTTGTGTGAGATACTAAT
          1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT

                                                   
       4059 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGATACTAAT
          1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT

                                           *      *
       4097 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
          1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT

                  *                         *       
       4136 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
          1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT

             *        *                
       4175 AACCGGGCTATGTCCCGAAGGCATTTG
          1 -TCCGGGCTAAG-CCCGAAGGCATTTG

       4202 AACGAGTAGC


Statistics
Matches: 162,  Mismatches: 15, Indels: 12
        0.86            0.08        0.06

Matches are distributed among these distances:
  38   37  0.23
  39   36  0.22
  40   78  0.48
  41   10  0.06
  42    1  0.01

ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26


Consensus pattern (39 bp):   
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT

Found at i:4223 original size:79 final size:79

Alignment explanation


    Indices: 4070--4234  Score: 210
    Period size: 79  Copynumber: 2.1  Consensus size: 79

       4060 CCGGGCTAAG

                                       *                        **           
       4070 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
          1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA

                       *  
       4135 ATCCGGGTTAAGTC
         66 ATCCGGGTTAAATC

                               *                 *                           
       4149 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
          1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C

              *             *
       4212 TATATCC-GGTTAAATT
         63 TAAATCCGGGTTAAATC

                   
       4228 CCGAAGG
          1 CCGAAGG

       4235 TACGTGATTT


Statistics
Matches: 75,  Mismatches: 8, Indels: 6
        0.84            0.09        0.07

Matches are distributed among these distances:
  78    2  0.03
  79   48  0.64
  80   25  0.33

ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25


Consensus pattern (79 bp):   
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.